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Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori.
- Published in:
- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-37975-y
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- Publication type:
- Article
Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco.
- Published in:
- BMC Genomics, 2019, v. 20, p. 1, doi. 10.1186/s12864-019-6341-6
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- Publication type:
- Article
iSyTE 2.0: a database for expression-based gene discovery in the eye.
- Published in:
- Nucleic Acids Research, 2018, v. 46, n. D1, p. D875, doi. 10.1093/nar/gkx837
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- Publication type:
- Article
PBrowse: a web-based platform for real-time collaborative exploration of genomic data.
- Published in:
- Nucleic Acids Research, 2017, v. 45, n. 9, p. 1, doi. 10.1093/nar/gkw1358
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- Publication type:
- Article
Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site.
- Published in:
- Nucleic Acids Research, 2016, v. 44, n. 3, p. 1411, doi. 10.1093/nar/gkv1466
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- Publication type:
- Article
Impact of sequencing depth in ChIP-seq experiments.
- Published in:
- Nucleic Acids Research, 2015, v. 43, n. 9, p. 1, doi. 10.1093/nar/gku178
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- Publication type:
- Article
Machine learning-coupled combinatorial mutagenesis enables resource-efficient engineering of CRISPR-Cas9 genome editor activities.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-29874-5
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- Publication type:
- Article
MQuad enables clonal substructure discovery using single cell mitochondrial variants.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28845-0
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- Publication type:
- Article
Generalized and scalable trajectory inference in single-cell omics data with VIA.
- Published in:
- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25773-3
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- Publication type:
- Article
FlowGrid enables fast clustering of very large single-cell RNA-seq data.
- Published in:
- Bioinformatics, 2022, v. 38, n. 1, p. 282, doi. 10.1093/bioinformatics/btab521
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- Publication type:
- Article
Efficient Differentiation of Steroidogenic and Germ-Like Cells from Epigenetically-Related iPSCs Derived from Ovarian Granulosa Cells.
- Published in:
- PLoS ONE, 2015, v. 10, n. 3, p. 1, doi. 10.1371/journal.pone.0119275
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- Publication type:
- Article
How Difficult Is Inference of Mammalian Causal Gene Regulatory Networks?
- Published in:
- PLoS ONE, 2014, v. 9, n. 11, p. 1, doi. 10.1371/journal.pone.0111661
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- Publication type:
- Article
An Antibody-Based Leukocyte-Capture Microarray for the Diagnosis of Systemic Lupus Erythematosus.
- Published in:
- PLoS ONE, 2013, v. 8, n. 3, p. 1, doi. 10.1371/journal.pone.0058199
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- Publication type:
- Article
An Evolutionarily Conserved Enhancer Regulates Bmp4 Expression in Developing Incisor and Limb Bud.
- Published in:
- PLoS ONE, 2012, v. 7, n. 6, p. 1, doi. 10.1371/journal.pone.0038568
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- Publication type:
- Article
Incidence of Emergency Department Visits for Sexual Abuse Among Youth in Hong Kong Before and During the COVID-19 Pandemic.
- Published in:
- JAMA Network Open, 2022, v. 5, n. 10, p. e2236278, doi. 10.1001/jamanetworkopen.2022.36278
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- Publication type:
- Article
Ultrafast clustering of single-cell flow cytometry data using FlowGrid.
- Published in:
- BMC Systems Biology, 2019, v. 13, p. N.PAG, doi. 10.1186/s12918-019-0690-2
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- Publication type:
- Article
Identification of active signaling pathways by integrating gene expression and protein interaction data.
- Published in:
- BMC Systems Biology, 2018, v. 12, n. 9, p. N.PAG, doi. 10.1186/s12918-018-0655-x
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- Publication type:
- Article
Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie.
- Published in:
- BMC Bioinformatics, 2014, v. 15, n. Suppl 16, p. 1, doi. 10.1186/1471-2105-15-S16-S15
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- Publication type:
- Article
Gene-gene interaction filtering with ensemble of filters.
- Published in:
- BMC Bioinformatics, 2011, v. 12, n. Suppl 1, p. 1, doi. 10.1186/1471-2105-12-S1-S10
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- Publication type:
- Article
A genetic ensemble approach for gene-gene interaction identification.
- Published in:
- BMC Bioinformatics, 2010, v. 11, p. 524, doi. 10.1186/1471-2105-11-524
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- Publication type:
- Article
A voting approach to identify a small number of highly predictive genes using multiple classifiers.
- Published in:
- BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-S1-S19
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- Publication type:
- Article
An innovative approach for testing bioinformatics programs using metamorphic testing.
- Published in:
- BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-24
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- Publication type:
- Article
PD-L1 regulates inflammatory programs of macrophages from human pluripotent stem cells.
- Published in:
- Life Science Alliance, 2024, v. 7, n. 2, p. 1, doi. 10.26508/lsa.202302461
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- Publication type:
- Article
Enhanced cardiac repair by telomerase reverse transcriptase over-expression in human cardiac mesenchymal stromal cells.
- Published in:
- Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-47022-w
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- Publication type:
- Article
An Embryonic and Induced Pluripotent Stem Cell Model for Ovarian Granulosa Cell Development and Steroidogenesis.
- Published in:
- Reproductive Sciences, 2018, v. 25, n. 5, p. 712, doi. 10.1177/1933719117725814
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- Publication type:
- Article
scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq.
- Published in:
- Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae011
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- Publication type:
- Article
Multi-omic profiling reveals associations between the gut mucosal microbiome, the metabolome, and host DNA methylation associated gene expression in patients with colorectal cancer.
- Published in:
- BMC Microbiology, 2020, v. 20, n. 1, p. 1, doi. 10.1186/s12866-020-01762-2
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- Publication type:
- Article
Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest.
- Published in:
- BMC Genomics, 2018, v. 19, p. 153, doi. 10.1186/s12864-017-4340-z
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- Publication type:
- Article
Deep Learning for Clinical Image Analyses in Oral Squamous Cell Carcinoma: A Review.
- Published in:
- 2021
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- Publication type:
- journal article
Machine learning application for the prediction of SARS-CoV-2 infection using blood tests and chest radiograph.
- Published in:
- Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-93719-2
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- Publication type:
- Article
Comparative analysis of metazoan chromatin organization.
- Published in:
- Nature, 2014, v. 512, n. 7515, p. 449, doi. 10.1038/nature13415
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- Publication type:
- Article
SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides.
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- Bioinformatics, 2006, v. 22, n. 17, p. 2162
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- Publication type:
- Article
Assessment of Intratumoral and Peritumoral Computed Tomography Radiomics for Predicting Pathological Complete Response to Neoadjuvant Chemoradiation in Patients With Esophageal Squamous Cell Carcinoma.
- Published in:
- JAMA Network Open, 2020, v. 3, n. 9, p. e2015927, doi. 10.1001/jamanetworkopen.2020.15927
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- Publication type:
- Article
Dynamic changes in antibiotic resistance genes and gut microbiota after Helicobacter pylori eradication therapies.
- Published in:
- Helicobacter, 2022, v. 27, n. 2, p. 1, doi. 10.1111/hel.12871
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- Publication type:
- Article
Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity.
- Published in:
- Nucleic Acids Research, 2023, v. 51, n. 11, p. e62, doi. 10.1093/nar/gkad307
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- Publication type:
- Article
Ularcirc: visualization and enhanced analysis of circular RNAs via back and canonical forward splicing.
- Published in:
- Nucleic Acids Research, 2019, v. 47, n. 20, p. e123, doi. 10.1093/nar/gkz718
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- Publication type:
- Article
StaVia: spatially and temporally aware cartography with higher-order random walks for cell atlases.
- Published in:
- Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03347-y
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- Publication type:
- Article
CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data.
- Published in:
- Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1188-0
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- Publication type:
- Article
Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context.
- Published in:
- PLoS Genetics, 2012, v. 8, n. 4, p. 1, doi. 10.1371/journal.pgen.1002646
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- Publication type:
- Article
Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding.
- Published in:
- Epigenetics & Chromatin, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13072-019-0273-x
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- Publication type:
- Article
ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis.
- Published in:
- BMC Genomics, 2011, v. 12, n. 1, p. 134, doi. 10.1186/1471-2164-12-134
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- Publication type:
- Article
A model selection approach to discover age-dependent gene expression patterns using quantile regression models.
- Published in:
- BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-S3-S16
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- Publication type:
- Article
Introduction to the Special Issue on GIW/ABACBS 2019.
- Published in:
- Journal of Bioinformatics & Computational Biology, 2020, v. 18, n. 01, p. N.PAG, doi. 10.1142/S0219720020020011
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- Publication type:
- Article
VERIFICATION OF PHYLOGENETIC INFERENCE PROGRAMS USING METAMORPHIC TESTING.
- Published in:
- Journal of Bioinformatics & Computational Biology, 2011, v. 9, n. 6, p. 729, doi. 10.1142/S021972001100563X
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- Publication type:
- Article
dv-trio: a family-based variant calling pipeline using DeepVariant.
- Published in:
- Bioinformatics, 2020, v. 36, n. 11, p. 3549, doi. 10.1093/bioinformatics/btaa116
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- Publication type:
- Article
PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells.
- Published in:
- Bioinformatics, 2020, v. 36, n. 9, p. 2778, doi. 10.1093/bioinformatics/btaa042
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- Publication type:
- Article
Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells.
- Published in:
- Bioinformatics, 2017, v. 33, n. 13, p. 1916, doi. 10.1093/bioinformatics/btx092
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- Publication type:
- Article
XGSA: A statistical method for cross-species gene set analysis.
- Published in:
- Bioinformatics, 2016, v. 32, n. 17, p. i620, doi. 10.1093/bioinformatics/btw428
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- Publication type:
- Article
hiHMM: Bayesian non-parametric joint inference of chromatin state maps.
- Published in:
- Bioinformatics, 2015, v. 31, n. 13, p. 2066, doi. 10.1093/bioinformatics/btv117
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- Publication type:
- Article
Erratum: Customising an antibody leukocyte capture microarray for systemic lupus erythematosus: Beyond biomarker discovery.
- Published in:
- Proteomics - Clinical Applications, 2010, v. 4, n. 6/7, p. 679
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- Publication type:
- Article